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BioC 3.0: CHECK report for r3Cseq on oaxaca

This page was generated on 2015-04-10 10:05:30 -0700 (Fri, 10 Apr 2015).

Package 709/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
r3Cseq 1.12.1
Supat Thongjuea
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/r3Cseq
Last Changed Rev: 97464 / Revision: 102249
Last Changed Date: 2014-12-07 15:30:30 -0800 (Sun, 07 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: r3Cseq
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch r3Cseq_1.12.1.tar.gz
StartedAt: 2015-04-10 02:32:37 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:37:15 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 278.1 seconds
RetCode: 0
Status:  OK 
CheckDir: r3Cseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch r3Cseq_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/r3Cseq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.12.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘GenomicRanges’ ‘Rsamtools’ ‘data.table’ ‘rtracklayer’ ‘VGAM’
  ‘qvalue’ ‘RColorBrewer’ ‘sqldf’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘r3Cseq’ can be installed ... [26s/28s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘RColorBrewer’ ‘Rsamtools’ ‘VGAM’ ‘data.table’
  ‘methods’ ‘qvalue’ ‘rtracklayer’ ‘sqldf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDomainogramNearViewpoint,r3Cseq: warning in axis(1, at = c(seq(0,
  1, by = 0.1)), lab = c(seq(-distance, distance, distance/5)),
  cex.axis = 0.8, las = 2): partial argument match of 'lab' to 'labels'
plotDomainogramNearViewpoint,r3Cseq: warning in axis(2, at = c(0, 1),
  lab = c(paste(maximum_window/1000, "Kb"), "2 Kb"), cex.axis = 0.8,
  las = 2): partial argument match of 'lab' to 'labels'
assign3CseqSigContact: no visible global function definition for
  ‘space’
assign3CseqSigContact: no visible global function definition for
  ‘vsmooth.spline’
assign3CseqSigContact: no visible global function definition for
  ‘qvalue’
assign3CseqSigContact: no visible binding for global variable
  ‘relative.position’
assign3CseqSigContact: no visible binding for global variable
  ‘chromosome’
assign3CseqSigContact: no visible global function definition for
  ‘RangedData’
assign3CseqSigContact: no visible global function definition for
  ‘IRanges’
excludeReadsNearViewpoint: no visible global function definition for
  ‘space’
excludeReadsNearViewpoint: no visible global function definition for
  ‘RangedData’
excludeReadsNearViewpoint: no visible global function definition for
  ‘IRanges’
excludeReadsNearViewpoint: no visible global function definition for
  ‘subjectHits’
excludeReadsNearViewpoint: no visible global function definition for
  ‘findOverlaps’
generate3CseqReport: no visible global function definition for ‘space’
get3CseqRefGene: no visible binding for global variable ‘hg18refGene’
get3CseqRefGene: no visible binding for global variable ‘hg19refGene’
get3CseqRefGene: no visible binding for global variable ‘mm9refGene’
getContrInteractionsInRefseq: no visible global function definition for
  ‘GRanges’
getContrInteractionsInRefseq: no visible global function definition for
  ‘space’
getContrInteractionsInRefseq: no visible global function definition for
  ‘IRanges’
getContrInteractionsInRefseq: no visible global function definition for
  ‘findOverlaps’
getContrInteractionsInRefseq: no visible global function definition for
  ‘queryHits’
getContrInteractionsInRefseq: no visible global function definition for
  ‘subjectHits’
getContrInteractionsInRefseq: no visible global function definition for
  ‘sqldf’
getExpInteractionsInRefseq: no visible global function definition for
  ‘GRanges’
getExpInteractionsInRefseq: no visible global function definition for
  ‘space’
getExpInteractionsInRefseq: no visible global function definition for
  ‘IRanges’
getExpInteractionsInRefseq: no visible global function definition for
  ‘findOverlaps’
getExpInteractionsInRefseq: no visible global function definition for
  ‘queryHits’
getExpInteractionsInRefseq: no visible global function definition for
  ‘subjectHits’
getExpInteractionsInRefseq: no visible global function definition for
  ‘sqldf’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getFragmentsPerWindow: no visible global function definition for
  ‘seqlengths’
getFragmentsPerWindow: no visible global function definition for
  ‘RangedData’
getFragmentsPerWindow: no visible global function definition for
  ‘IRanges’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
getPowerLawFittedCoeficient: no visible global function definition for
  ‘data.table’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘num’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘nr_reads’
getPowerLawFittedCoeficient: no visible global function definition for
  ‘setkey’
getPowerLawFittedCoeficient: no visible global function definition for
  ‘setnames’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getViewpoint: no visible global function definition for ‘matchPattern’
getViewpoint: no visible global function definition for ‘DNAString’
getViewpoint: no visible global function definition for
  ‘reverseComplement’
getViewpoint: no visible global function definition for ‘RangedData’
getViewpoint: no visible global function definition for ‘IRanges’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘space’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘seqnames’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘seqlengths’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘RangedData’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘IRanges’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘countOverlaps’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘vsmooth.spline’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘qvalue’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘space’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘seqlengths’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘chromosome’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘brewer.pal’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘exp_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘contr_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘log2fold’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsPerChromosome: no visible global function definition
  for ‘seqlengths’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsPerChromosome: no visible global function definition
  for ‘space’
plotInteractionsPerChromosome: no visible global function definition
  for ‘brewer.pal’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotOverviewInteractions: no visible global function definition for
  ‘seqlengths’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotOverviewInteractions: no visible global function definition for
  ‘brewer.pal’
plotOverviewInteractions: no visible global function definition for
  ‘space’
powerLawFittedRPM: no visible global function definition for ‘zeta’
calculateBatchRPM,r3CseqInBatch: no visible global function definition
  for ‘space’
calculateBatchRPM,r3CseqInBatch: no visible global function definition
  for ‘RangedData’
calculateBatchRPM,r3CseqInBatch: no visible global function definition
  for ‘IRanges’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  ‘space’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  ‘RangedData’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  ‘IRanges’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  ‘export’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for ‘RleList’
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for ‘seqlengths’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for ‘seqlevels<-’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for ‘seqlengths<-’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for ‘coverage’
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
  variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for ‘export’
exportBatchInteractions2text,r3CseqInBatch: no visible global function
  definition for ‘space’
exportInteractions2text,r3Cseq: no visible global function definition
  for ‘space’
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for ‘space’
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for ‘qvalue’
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for ‘RangedData’
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for ‘IRanges’
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for ‘ScanBamParam’
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for ‘scanBamFlag’
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for ‘scanBam’
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for ‘width’
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for ‘GRanges’
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for ‘IRanges’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for ‘RangedData’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for ‘IRanges’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for ‘space’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for ‘countOverlaps’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for ‘space’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for ‘countOverlaps’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for ‘RangedData’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for ‘IRanges’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  global function definition for ‘matchPattern’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
  binding for global variable ‘enzyme’
getRawReads,r3Cseq: no visible global function definition for
  ‘ScanBamParam’
getRawReads,r3Cseq: no visible global function definition for
  ‘scanBamFlag’
getRawReads,r3Cseq: no visible global function definition for ‘scanBam’
getRawReads,r3Cseq: no visible global function definition for ‘width’
getRawReads,r3Cseq: no visible global function definition for ‘GRanges’
getRawReads,r3Cseq: no visible global function definition for ‘IRanges’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for ‘RangedData’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for ‘IRanges’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for ‘countOverlaps’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for ‘space’
getReadCountPerWindow,r3Cseq: no visible global function definition for
  ‘countOverlaps’
getReadCountPerWindow,r3Cseq: no visible global function definition for
  ‘RangedData’
getReadCountPerWindow,r3Cseq: no visible global function definition for
  ‘space’
getReadCountPerWindow,r3Cseq: no visible global function definition for
  ‘IRanges’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘space’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘seqlengths’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘chromosome’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘brewer.pal’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.

r3Cseq.Rcheck/00install.out:

* installing *source* package ‘r3Cseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (r3Cseq)

r3Cseq.Rcheck/r3Cseq-Ex.timings:

nameusersystemelapsed
calculateBatchRPM0.0000.0000.001
calculateRPM0.0010.0000.001
contrInteractionRegions0.0010.0000.000
contrRPM0.0010.0000.000
contrRawData0.0010.0000.001
contrReadCount0.0010.0010.001
expInteractionRegions0.0010.0000.000
expRPM0.0010.0000.001
expRawData0.0010.0000.001
expReadCount0.0010.0000.001
export3Cseq2bedGraph0.0010.0000.000
export3CseqRawReads2bedGraph000
exportBatchInteractions2text0.0010.0000.001
exportInteractions2text0.0010.0000.000
generate3CseqReport0.0010.0000.001
getBatchInteractions0.0010.0010.001
getBatchRawReads0.0010.0000.000
getBatchReadCountPerRestrictionFragment0.0010.0000.001
getBatchReadCountPerWindow0.0010.0000.001
getContrInteractionsInRefseq0.0010.0000.000
getExpInteractionsInRefseq0.0010.0000.001
getInteractions0.0010.0000.001
getRawReads0.0010.0000.000
getReadCountPerRestrictionFragment0.0000.0000.001
getReadCountPerWindow000
getViewpoint0.0000.0000.001
plotDomainogramNearViewpoint0.0010.0000.001
plotInteractionsNearViewpoint0.0010.0000.001
plotInteractionsPerChromosome0.0010.0000.000
plotOverviewInteractions0.0000.0000.001
r3Cseq-class0.0010.0000.000
r3CseqCommon-class0.0010.0000.001
r3CseqInBatch-class0.0000.0010.001